3pce - Revision history

OCA at 07:05, 27 September 2023

2023-09-27T07:05:33Z

←Older revision		Revision as of 07:05, 27 September 2023
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	<StructureSection load='3pce' size='340' side='right'caption='[[3pce]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='3pce' size='340' side='right'caption='[[3pce]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pce]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PCE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3PCE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pce]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PCE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PCE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3HP:3-HYDROXYPHENYLACETATE'>3HP</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.06Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protocatechuate_3,4-dioxygenase Protocatechuate 3,4-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.3 1.13.11.3] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3HP:3-HYDROXYPHENYLACETATE'>3HP</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3pce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pce OCA], [~~http~~://pdbe.org/3pce PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3pce RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3pce PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3pce ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pce OCA], [https://pdbe.org/3pce PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pce RCSB], [https://www.ebi.ac.uk/pdbsum/3pce PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pce ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PCXA_PSEPU PCXA_PSEPU~~]] Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway. [[http://www.uniprot.org/uniprot/PCXB_PSEPU PCXB_PSEPU]~~] Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway.	+	[https://www.uniprot.org/uniprot/PCXA_PSEPU PCXA_PSEPU] Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Protocatechuate 3,4-dioxygenase]]
	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]
-	[[Category: Elango, N]]	+	[[Category: Elango N]]
-	[[Category: Lipscomb~~, J D~~]]	+	[[Category: Lipscomb JD]]
-	[[Category: Ohlendorf~~, D H~~]]	+	[[Category: Ohlendorf DH]]
-	[[Category: Orville~~, A M]]~~	+	[[Category: Orville AM]]
-	~~[[Category: Dioxygenase]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Metalloprotein]]~~	+
-	~~[[Category: Nonheme]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 13:57, 25 December 2019

2019-12-25T13:57:07Z

←Older revision		Revision as of 13:57, 25 December 2019
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	==STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYPHENYLACETATE==		==STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYPHENYLACETATE==
-	<StructureSection load='3pce' size='340' side='right' caption='[[3pce]], [[Resolution\|resolution]] 2.06Å' scene=''>	+	<StructureSection load='3pce' size='340' side='right'caption='[[3pce]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3pce]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PCE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PCE FirstGlance]. <br>		<table><tr><td colspan='2'>[[3pce]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PCE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PCE FirstGlance]. <br>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pc/3pce_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pc/3pce_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	</div>		</div>
	<div class="pdbe-citations 3pce" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3pce" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Protocatechuate 3,4-dioxygenase]]		[[Category: Protocatechuate 3,4-dioxygenase]]
	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]

OCA at 07:16, 29 November 2017

2017-11-29T07:16:58Z

←Older revision		Revision as of 07:16, 29 November 2017
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		+
	==STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYPHENYLACETATE==		==STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYPHENYLACETATE==
	<StructureSection load='3pce' size='340' side='right' caption='[[3pce]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='3pce' size='340' side='right' caption='[[3pce]], [[Resolution\|resolution]] 2.06Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3HP:3-HYDROXYPHENYLACETATE'>3HP</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3HP:3-HYDROXYPHENYLACETATE'>3HP</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protocatechuate_3,4-dioxygenase Protocatechuate 3,4-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.3 1.13.11.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protocatechuate_3,4-dioxygenase Protocatechuate 3,4-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.3 1.13.11.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3pce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pce OCA], [http://pdbe.org/3pce PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pce RCSB], [http://www.ebi.ac.uk/pdbsum/3pce PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3pce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pce OCA], [http://pdbe.org/3pce PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pce RCSB], [http://www.ebi.ac.uk/pdbsum/3pce PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pce ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 3pce" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3pce" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Dioxygenase\|Dioxygenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:50, 9 February 2016

2016-02-09T09:50:19Z

←Older revision		Revision as of 09:50, 9 February 2016
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3HP:3-HYDROXYPHENYLACETATE'>3HP</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3HP:3-HYDROXYPHENYLACETATE'>3HP</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protocatechuate_3,4-dioxygenase Protocatechuate 3,4-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.3 1.13.11.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protocatechuate_3,4-dioxygenase Protocatechuate 3,4-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.3 1.13.11.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3pce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pce OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pce RCSB], [http://www.ebi.ac.uk/pdbsum/3pce PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3pce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pce OCA], [http://pdbe.org/3pce PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pce RCSB], [http://www.ebi.ac.uk/pdbsum/3pce PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3pce ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3pce" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 06:04, 25 December 2014

2014-12-25T06:04:54Z

←Older revision		Revision as of 06:04, 25 December 2014
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3pce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pce OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pce RCSB], [http://www.ebi.ac.uk/pdbsum/3pce PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3pce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pce OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pce RCSB], [http://www.ebi.ac.uk/pdbsum/3pce PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PCXA_PSEPU PCXA_PSEPU]] Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway. [[http://www.uniprot.org/uniprot/PCXB_PSEPU PCXB_PSEPU]] Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:04, 19 December 2014

2014-12-19T07:04:03Z

←Older revision		Revision as of 07:04, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3pce\| PDB=3pce \| SCENE= }}~~	+	==STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYPHENYLACETATE==
-	===STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYPHENYLACETATE===	+	<StructureSection load='3pce' size='340' side='right' caption='[[3pce]], [[Resolution\|resolution]] 2.06Å' scene=''>
-	~~{{ABSTRACT_PUBMED_9254599}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3pce]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PCE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PCE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3HP:3-HYDROXYPHENYLACETATE'>3HP</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protocatechuate_3,4-dioxygenase Protocatechuate 3,4-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.3 1.13.11.3] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3pce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pce OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pce RCSB], [http://www.ebi.ac.uk/pdbsum/3pce PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pc/3pce_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protocatechuate 3,4-dioxygenase (3,4-PCD) catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis, cis-muconate. Crystal structures of Pseudomonas putida3,4-PCD [quaternary structure of (alphabetaFe3+)12] complexed with seven competitive inhibitors [3-hydroxyphenylacetate (MHP), 4-hydroxyphenylacetate (PHP), 3-hydroxybenzoate (MHB), 4-hydroxybenzoate (PHB), 3-fluoro-4-hydroxybenzoate (FHB), 3-chloro-4-hydroxybenzoate (CHB), and 3-iodo-4-hydroxybenzoate (IHB)] are reported at 2.0-2.2 A resolution with R-factors of 0. 0.159-0.179. The inhibitors bind in a narrow active site crevasse lined with residues that provide a microenvironment that closely matches the chemical characteristics of the inhibitors. This results in as little as 20% solvent-exposed surface area for the higher-affinity inhibitors (PHB, CHB, and FHB). In uncomplexed 3,4-PCD, the active site Fe3+ is bound at the bottom of the active site crevasse by four endogenous ligands and a solvent molecule (Wat827). The orientations of the endogenous ligands are relatively unperturbed in each inhibitor complex, but the inhibitors themselves bind to or near the iron in a range of positions, all of which perturb the position of Wat827. The three lowest-affinity inhibitors (MHP, PHP, and IHB) yield distorted trigonal bipyramidal iron coordination geometry in which the inhibitor C4-phenolate group displaces the solvent ligand. MHB binds within the active site, but neither its C3-OH group nor the solvent molecule binds to the iron. The C4-phenolate group of the three highest-affinity inhibitors (PHB, CHB, and FHB) coordinates the Fe3+ adjacent to Wat827, resulting in a shift in its position to yield a six-coordinate distorted octahedral geometry. The range of inhibitor orientations may mimic the mechanistically significant stages of substrate binding to 3, 4-PCD. The structure of the final substrate complex is reported in the following paper [Orville, A. M., Lipscomb, J. D., & Ohlendorf, D. H. (1997) Biochemistry 36, 10052-10066].

-	~~==Function==~~	+	Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site.,Orville AM, Elango N, Lipscomb JD, Ohlendorf DH Biochemistry. 1997 Aug 19;36(33):10039-51. PMID:9254599<ref>PMID:9254599</ref>
-	~~[[http~~:~~//www~~.~~uniprot~~.~~org/uniprot/PCXA_PSEPU PCXA_PSEPU]] Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta~~-~~ketoadipate pathway~~. ~~[[http~~:/~~/www.uniprot.org/uniprot/PCXB_PSEPU PCXB_PSEPU]] Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway.~~	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3pce]] is~~ a ~~12 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_putida Pseudomonas putida]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3PCE OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:009254599</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Dioxygenase\|Dioxygenase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Protocatechuate 3,4-dioxygenase]]		[[Category: Protocatechuate 3,4-dioxygenase]]
	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]
-	[[Category: Elango, N.]]	+	[[Category: Elango, N]]
-	[[Category: Lipscomb, J D.]]	+	[[Category: Lipscomb, J D]]
-	[[Category: Ohlendorf, D H.]]	+	[[Category: Ohlendorf, D H]]
-	[[Category: Orville, A M.]]	+	[[Category: Orville, A M]]
	[[Category: Dioxygenase]]		[[Category: Dioxygenase]]
	[[Category: Iron]]		[[Category: Iron]]

OCA: Protected "3pce" [edit=sysop:move=sysop]

2013-05-02T08:14:54Z

Protected "3pce" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:14, 2 May 2013

OCA at 08:14, 2 May 2013

2013-05-02T08:14:52Z

←Older revision		Revision as of 08:14, 2 May 2013
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-	{{Seed}}
-	[[Image:3pce.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3pce", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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	{{STRUCTURE_3pce\| PDB=3pce \| SCENE= }}		{{STRUCTURE_3pce\| PDB=3pce \| SCENE= }}
-
	===STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYPHENYLACETATE===		===STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYPHENYLACETATE===
		+	{{ABSTRACT_PUBMED_9254599}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/PCXA_PSEPU PCXA_PSEPU]] Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway. [[http://www.uniprot.org/uniprot/PCXB_PSEPU PCXB_PSEPU]] Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway.
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_9254599}}, adds~~ the ~~Publication Abstract to~~ the ~~page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov), where 9254599 is~~ the ~~PubMed ID number.~~	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_9254599}}~~	+

	==About this Structure==		==About this Structure==
-	~~3PCE~~ is a 12 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PCE OCA].	+	[[3pce]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PCE OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~9254599~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:009254599</ref><references group="xtra"/><references/>
	[[Category: Protocatechuate 3,4-dioxygenase]]		[[Category: Protocatechuate 3,4-dioxygenase]]
	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]
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	[[Category: Nonheme]]		[[Category: Nonheme]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 08:54:58 2009''

OCA at 06:54, 17 February 2009

2009-02-17T06:54:58Z

←Older revision		Revision as of 06:54, 17 February 2009
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	==About this Structure==		==About this Structure==
-	3PCE is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PCE OCA].	+	3PCE is a 12 chains structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PCE OCA].

	==Reference==		==Reference==
-	Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site., Orville AM, Elango N, Lipscomb JD, Ohlendorf DH, Biochemistry. 1997 Aug 19;36(33):10039-51. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/9254599 9254599]~~	+	<ref group="xtra">PMID:9254599</ref><references group="xtra"/>
-	~~[[Category: Protein complex]]~~	+
	[[Category: Protocatechuate 3,4-dioxygenase]]		[[Category: Protocatechuate 3,4-dioxygenase]]
	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]
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	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3 13~~:00:~~03 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 08:54:58 2009''

OCA at 10:00, 3 July 2008

2008-07-03T10:00:03Z

←Older revision		Revision as of 10:00, 3 July 2008
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-	[[Image:3pce.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:3pce.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_3pce\| PDB=3pce \| SCENE= }}		{{STRUCTURE_3pce\| PDB=3pce \| SCENE= }}

-	~~'''~~STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYPHENYLACETATE~~'''~~	+	===STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYPHENYLACETATE===


-	~~==Overview==~~	+	<!--
-	~~Protocatechuate 3,4~~-~~dioxygenase (3,4~~-PCD) catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis, cis-muconate. Crystal structures of Pseudomonas putida3,4-PCD [quaternary structure of (alphabetaFe3+)12] complexed with seven competitive inhibitors [3-hydroxyphenylacetate (MHP), 4-hydroxyphenylacetate (PHP), 3-hydroxybenzoate (MHB), 4-hydroxybenzoate (PHB), 3-fluoro-4-hydroxybenzoate (FHB), 3-chloro-4-hydroxybenzoate (CHB), and 3-iodo-4-hydroxybenzoate (IHB)] are reported at 2.0-2.2 A resolution with R-factors of 0. 0.159-0.179. The inhibitors bind in a narrow active site crevasse lined with residues that provide a microenvironment that closely matches the chemical characteristics of the inhibitors. This results in as little as 20% solvent-exposed surface area for the higher-affinity inhibitors (PHB, ~~CHB~~, and FHB). In uncomplexed 3,4-PCD, the active site Fe3+ is bound at the bottom of the active site crevasse by four endogenous ligands and a solvent molecule (Wat827). The orientations of the endogenous ligands are relatively unperturbed in each inhibitor complex, but the ~~inhibitors themselves bind~~ to ~~or near~~ the ~~iron in a range of positions, all of which perturb the position of Wat827. The three lowest-affinity inhibitors~~ (~~MHP, PHP, and IHB) yield distorted trigonal bipyramidal iron coordination geometry in which the inhibitor C4-phenolate group displaces the solvent ligand~~. ~~MHB binds within the active site, but neither its C3-OH group nor the solvent molecule binds to the iron~~. ~~The C4-phenolate group of the three highest-affinity inhibitors (PHB, CHB, and FHB~~) ~~coordinates the Fe3+ adjacent to Wat827~~, resulting in a shift in its position to yield a six-coordinate distorted octahedral geometry. The range of inhibitor orientations may mimic the mechanistically significant stages of substrate binding to 3, 4-PCD. The structure of the final substrate complex is ~~reported in~~ the ~~following paper [Orville, A~~. ~~M., Lipscomb, J. D., & Ohlendorf, D. H. (1997) Biochemistry 36, 10052~~-~~10066].~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_9254599}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9254599 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_9254599}}

	==About this Structure==		==About this Structure==
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	[[Category: Nonheme]]		[[Category: Nonheme]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:09:15 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 13:00:03 2008''